View source for 1vc5

==Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in EDTA solution==
<StructureSection load='1vc5' size='340' side='right' caption='[[1vc5]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1vc5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VC5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1drz|1drz]], [[1cx0|1cx0]], [[1vbx|1vbx]], [[1vby|1vby]], [[1vbz|1vbz]], [[1vc0|1vc0]], [[1sjf|1sjf]], [[1vc6|1vc6]], [[1vc7|1vc7]]</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vc5 OCA], [http://pdbe.org/1vc5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vc5 RCSB], [http://www.ebi.ac.uk/pdbsum/1vc5 PDBsum]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>  
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/1vc5_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vc5 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.

A conformational switch controls hepatitis delta virus ribozyme catalysis.,Ke A, Zhou K, Ding F, Cate JH, Doudna JA Nature. 2004 May 13;429(6988):201-5. PMID:15141216<ref>PMID:15141216</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1vc5" style="background-color:#fffaf0;"></div>

==See Also==
*[[Nucleoprotein|Nucleoprotein]]
*[[Ribozyme|Ribozyme]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Human]]
[[Category: Cate, J H.D]]
[[Category: Ding, F]]
[[Category: Doudna, J A]]
[[Category: Ke, A]]
[[Category: Zhou, K]]
[[Category: Hdv]]
[[Category: Precursor]]
[[Category: Ribozyme]]
[[Category: Rna]]
[[Category: Translation-rna complex]]
[[Category: U1a]]